Contacts of the helix formed by residues 407 - 411 (chain F) in PDB entry 4DVQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 407 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374F ARG 4.4 0.5 - - - +
377F PRO* 3.9 17.4 - - + +
379F GLY 3.3 20.9 - - - +
380F LEU 2.8 17.6 + - - +
381F PHE 4.7 0.2 - - - -
382F LEU* 4.1 23.1 - - + +
405F VAL* 3.4 7.6 + - + +
406F PHE* 1.3 69.4 - - - +
408F TYR* 1.3 58.5 + - - +
409F SER 3.1 2.5 - - - -
410F LEU* 3.6 15.0 - - + +
411F GLY* 2.7 30.0 + - - -
441F VAL* 3.4 48.2 - - + +
442F PRO* 4.3 14.8 - - + +
601F HEM 5.1 0.9 - - + -
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Residues in contact with TYR 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F HIS* 3.9 22.5 + + + -
66F LEU* 3.7 20.7 - - + +
69F HIS* 4.1 22.7 - + + -
374F ARG 5.0 0.2 - - - -
375F LEU 4.0 7.6 - - - -
377F PRO* 3.7 10.6 - - + +
380F LEU* 3.6 14.5 + - + -
406F PHE* 3.4 29.1 - + + -
407F LEU* 1.3 78.8 - - - +
409F SER* 1.3 57.1 + - - +
411F GLY* 3.8 0.7 + - - -
412F ARG* 3.2 81.8 + - - +
483F MET* 5.1 8.1 - - + +
489F LEU* 4.2 19.1 - - + -
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Residues in contact with SER 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F HIS* 2.4 39.3 + - - -
72F PHE* 4.1 3.7 - - - +
92F MET* 3.6 31.1 - - - +
406F PHE* 2.9 29.2 - - - -
407F LEU 3.1 0.2 - - - -
408F TYR* 1.3 73.9 - - - +
410F LEU* 1.3 71.4 + - - +
411F GLY 3.0 1.3 - - - -
412F ARG* 2.8 12.5 + - - +
413F ASN 3.1 9.2 + - - -
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Residues in contact with LEU 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F MET* 3.4 26.0 - - - +
94F PRO* 4.1 12.3 - - + -
97F VAL* 3.9 12.8 - - + -
405F VAL* 3.9 16.2 - - + -
406F PHE 3.2 15.6 + - - +
407F LEU* 3.6 15.7 - - + +
409F SER* 1.3 77.1 - - - +
411F GLY* 1.3 63.4 + - - +
412F ARG 3.0 1.4 + - - -
413F ASN* 3.2 14.9 + - + +
416F LEU* 4.0 24.0 - - + -
417F PHE* 3.6 7.4 - - + -
438F PHE 5.5 2.5 - - - +
439F HIS 5.0 7.6 - - - +
441F VAL* 3.8 28.9 - - + -
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Residues in contact with GLY 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374F ARG* 2.9 55.1 + - - +
407F LEU 2.7 17.6 + - - -
408F TYR 4.1 0.7 - - - -
410F LEU* 1.3 78.8 - - - +
412F ARG* 1.3 59.8 + - - +
413F ASN 3.6 0.7 - - - -
417F PHE* 3.3 12.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il